Use of IRAP and REMAP markers to interpret the population structure of Linum usitatissimum from Iran

Flax (Linum usitatissimum L.) is the third largest natural fiber crop in the world. The flax genome shows environmentally induced heritable genomic changes. The activation of transposable elements has been proposed and identified as the mechanism behind this genotypic plasticity. Transposable elements, particularly the retrotransposons, generates genomic diversity by replication which makes them an excellent source of molecular markers. Inter-retrotransposon amplified polymorphism (IRAP) and the retrotransposon-microsatellite amplified polymorphism (REMAP) markers were used to assess the insertional polymorphism of LTR retrotransposons and genetic diversity in 80 genotypes of L. usitatissimum collected from Iran. A total of 77 and 133 loci were amplified using 7 IRAP and 13 REMAP primers, respectively. Percentage of polymorphic loci (PPL) for IRAP and REMAP markers were 53.25% and 58.92%, respectively. Average of expected heterozygosity (He), number of effective alleles (Ne) and Shannon’s information index (I) for IRAP markers were slightly more than those of REMAP markers. A high level of intra-population genetic differentiation was found, which is supported by a moderate level of gene flow among populations. A model-based Bayesian approach and cluster analysis using Minimum Evolution (ME) algorithm distinguished genotypes collected from Alborz region from those collected from Zagros region. Mantel test between genetic and geographical distances of populations revealed low but significant correlation coefficient (r = 0.36, P ≤ 0.05). The results demonstrated that molecular markers developed based on active LTR retrotransposons in flax could be used as relatively reliable tools to analysis population structure in L. usitatissimum.